Jul 2026· Journal of Clinical Investigation· 0 citations
Medicine
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) accounts for 5-10% of prevalent end-stage kidney failure (ESKD). ADPKD cysts result from a loss of sufficient functional expression of PKD1/Polycystin-1 (PC1) in approximately 80% of families. Kidney disease severity correlates with the extent to which PC1 dosage is reduced below a critical level, and evidence suggests therapeutic benefit from increasing PC1 expression in these conditions. Upstream open reading frame (uORF) translation can reduce translation of a protein's coding sequence. Ribosome profiling data and bioinformatic predictions suggested the presence of conserved PKD1 uORFs, so we sought to explore their biological role. We generated luciferase reporters and two humanized PKD1 5'UTR mouse models with or without single nucleotide edits removing uORF start codons ("delta-uORF") to define active uORFs and test their impact on PC1 translation. PKD1 uORF start codons can robustly initiate translation and delta-uORF conveys a 2-4-fold increase in PC1 protein expression and resultant prevention of kidney cysts in Dnajb11 as well as in Pkd1 missense models. PKD1 uORF1-blocking steric antisense oligonucleotides (ASOs) substantially increase PC1 expression in vitro. PKD1 uORFs play an important role in the low basal expression of wild-type PKD1, and their inhibition represents an opportunity to therapeutically increase PC1 translation in polycystic kidney and liver disease resulting from reduced dosage of PC1.
Automated renal tubule and cyst quantification (ARTCyQ), a novel machine-learning pipeline to analyze immunofluorescent stainings, revealed increasing ambiguity in nephron segment identity and activation of ADPKD-related pathways, including YAP signaling.
Céline Gagnieux, F. Bernet, Lona J Kroese et al.· iScience· 0 citations
Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome. A cluster of frameshift-causing C-terminal deletions (CTDs) removes ~100 amino acids and accounts for approximately 10% of RTT-causing mutations. Their pathogenicity is unexpected because this C-terminal domain is dispensable in mice. Analysis of pathogenic and benign human MECP2 variants reveals that some individuals with apparently typical CTDs do not develop Rett syndrome, confirming that C-terminal truncations are not intrinsically pathogenic. Using human sequence data and mouse models we show that pathogenicity results from a marked reduction in MeCP2 levels and depends on the presence of a proline proline stop motif (-PPX) generated by a shift to the +2 reading frame. CTDs that shift to the +1 frame avoid this motif and are benign. Replacing the stop codon of the PPX motif with tryptophan restores MeCP2 expression and rescues RTT-like phenotypes in a CTD mouse model. An adenine base editor efficiently introduces this substitution in cultured cells. These findings define a reliable prognostic distinction between benign and pathogenic CTDs and establish a potential editing strategy for correcting disease-causing CTD mutations.
Jacky Guy, E. Hein, Beatrice K. Alexander-Howden et al.· eLife· 0 citations
Evidence is provided that biallelic CTNNA3 splice‐disrupting variants can cause human cardiomyopathy driven by ICD dysfunction, and the dissociation between ventricular recovery and persistent arrhythmia highlights the complex phenotypic spectrum of CTNNA3‐related disease.
Stefania Martino, Mara Doimo, M. Iacoviello et al.· Human Mutation· 0 citations
It is demonstrated that expanded DMPK transcript levels modulate free MBNL1 concentration and alternative splicing in a dose-dependent manner, underscoring the central role of repeat RNA expression in DM1 pathogenesis.
Lise Ripken, Thomas D. Hoekman, M. Willemse et al.· Human Molecular Genetics· 0 citations
These results demonstrate that ABE can effectively target the LMNA c.745C>T mutation but also reveal the significant impact of bystander edits on cellular physiology, underscoring the necessity of precise editing technologies to ensure both efficacy and safety in future clinical translation.
M. Santafé, I. Hernández, D. Mazzeo et al.· bioRxiv· 0 citations
Alternative polyadenylation (APA) is increasingly recognized as a pervasive oncogenic mechanism that reshapes post-transcriptional gene regulation and promotes tumor aggressiveness. Whether APA contributes to the dysregulation of
NFYA
—encoding the regulatory subunit of the oncogenic transcription factor NF-Y—in prostate cancer (PCa) remains largely uncharacterized.
We interrogated bulk, single cell and 3’-end RNA-sequencing data from PCa cell lines and patient samples to re-annotate and quantify the usage of
NFYA
3′UTRs. The functional consequences of APA were assessed using reporter assays.
NFYA
APA was experimentally reprogrammed using CRISPR/Cas9-mediated deletion and antisense oligonucleotide (ASO)-based masking of polyadenylation signals, followed by in vitro and in vivo phenotypic analyses.
Four functional
NFYA
3′UTR isoforms were identified, with one predominantly used across cell lines and tissues. PCa displayed pervasive
NFYA
3′UTR shortening, which correlated with tumor grade and metastatic disease, increased NF-YA protein abundance, and enhanced proliferation. 3′UTR lengthening was instead observed upon induction of cellular quiescence or after Enzalutamide treatment. Mechanistically, 3′UTR lengthening reduced NF-YA protein expression through decreased mRNA stability, impaired translation, and enhanced nuclear retention, rather than increased miRNA-mediated repression. Enforced
NFYA
3′UTR lengthening in PCa cells via CRISPR/Cas9 or ASOs diminished NF-YA protein levels and suppressed aggressive tumor traits both in vitro and in vivo.
These findings establish
NFYA
APA as a critical determinant of NF-YA oncogenic output and downstream tumor-promoting programs, and as a previously unrecognized driver of PCa progression. Importantly, they provide proof-of-concept for gene-specific, APA-directed therapeutic strategies. ASO-mediated modulation of polyadenylation indeed emerges as a clinically translatable approach to fine-tune oncogene expression, thus opening new avenues for RNA-based precision interventions in aggressive PCa.
Giulia Pagani, Chiara Casirati, Cecilia Pandini et al.· Journal of Experimental &...· 0 citations
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